Merge pull request #1138 from veg/develop

2.5.10 rc

CMakeLists.txt

@@ -617,6 +617,6 @@ add_test (BGM HYPHYMP tests/hbltests/libv3/BGM.wbf)
 add_test (CONTRAST-FEL HYPHYMP tests/hbltests/libv3/CFEL.wbf)
 add_test (GARD HYPHYMP tests/hbltests/libv3/GARD.wbf)
 add_test (FADE HYPHYMP tests/hbltests/libv3/FADE.wbf)
-add_test (ABSREL HYPHYMP tests/hbltests/libv3/aBSREL.wbf)
-add_test (ABSREL-MH HYPHYMP tests/hbltests/libv3/aBSREL-MH.wbf)
+add_test (NAME ABSREL COMMAND HYPHYMP tests/hbltests/libv3/ABSREL.wbf)
+add_test (NAME ABSREL-MH COMMAND HYPHYMP tests/hbltests/libv3/ABSREL-MH.wbf)
 

res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf

@@ -171,10 +171,14 @@ function models.codon.MG_REV.set_branch_length(model, value, parameter) {
                 }
             } else {
                 models.codon.MG_REV.set_branch_length.lp = 0;
+
+
                 if (parameters.IsIndependent(models.codon.MG_REV.set_branch_length.alpha.p)) {
                     Eval(models.codon.MG_REV.set_branch_length.alpha.p + ":=(" + value[terms.model.branch_length_scaler] + ")*" + value[terms.branch_length]);
                     models.codon.MG_REV.set_branch_length.lp += 1;
+
                 }
+
                 if (parameters.IsIndependent(models.codon.MG_REV.set_branch_length.beta.p)) {
                     Eval(models.codon.MG_REV.set_branch_length.beta.p + ":=(" + value[terms.model.branch_length_scaler] + ")*" + value[terms.branch_length]);
                     models.codon.MG_REV.set_branch_length.lp += 1;

res/TemplateBatchFiles/libv3/models/parameters.bf

@@ -494,7 +494,7 @@ lfunction parameters.IsIndependent(parameter) {
 
     GetString(info, ^ parameter, -1);
 
-    if (Type(info) == "AssociativeList") {
+    if (Type(info) == "AssociativeList") {    
         return (utility.CheckKey(info, "Local", "Matrix") && utility.CheckKey(info, "Global", "Matrix")) == FALSE;
     }
     return TRUE;

res/TemplateBatchFiles/libv3/tasks/estimators.bf

@@ -2,6 +2,7 @@ LoadFunctionLibrary("../models/model_functions.bf");
 LoadFunctionLibrary("../models/DNA/GTR.bf");
 LoadFunctionLibrary("../convenience/regexp.bf");
 LoadFunctionLibrary("mpi.bf");
+LoadFunctionLibrary("libv3/convenience/math.bf");
 LoadFunctionLibrary("libv3/all-terms.bf");
 
 
@@ -44,6 +45,21 @@ lfunction estimators.RestoreLFStateFromSnapshot(lf_id, snapshot) {
     }
 }
 
+lfunction estimators.ConstrainAndRunLRT (lf_id, constraint) {
+    savedMLES = estimators.TakeLFStateSnapshot (lf_id);
+    currentLL = estimators.ComputeLF (lf_id);
+
+    df = Call (constraint, TRUE);
+    Optimize (res, ^lf_id);
+    lrt = math.DoLRT (res[1][0],currentLL,df);
+
+    estimators.RestoreLFStateFromSnapshot (lf_id, savedMLES);
+
+    Call (constraint, FALSE);
+
+    return lrt;
+}
+
 /**
  * @name estimators.GetGlobalMLE
  * @param {Dictionary} results
@@ -445,6 +461,7 @@ function estimators.ApplyExistingEstimatesToTree (_tree_name, model_descriptions
                             _set_branch_length_to[terms.branch_length] = _existing_estimate[terms.fit.MLE];
                             _set_branch_length_to[terms.model.branch_length_scaler] = _application_type;
                             keep_track_of_proportional_scalers[_application_type] = 1;
+
                         }
                     }
                 }
@@ -525,45 +542,6 @@ function estimators.ApplyExistingEstimates(likelihood_function_id, model_descrip
 
 
 
-            /*
-            ExecuteCommands("GetInformation (estimators.ApplyExistingEstimates.map, `_tree_name`);");
-            estimators.ApplyExistingEstimates.branch_names = Rows(estimators.ApplyExistingEstimates.map);
-
-            for (estimators.ApplyExistingEstimates.b = 0; estimators.ApplyExistingEstimates.b < Abs(estimators.ApplyExistingEstimates.map); estimators.ApplyExistingEstimates.b += 1) {
-                _branch_name = estimators.ApplyExistingEstimates.branch_names[estimators.ApplyExistingEstimates.b];
-
-                if ((initial_values[terms.branch_length])[estimators.ApplyExistingEstimates.i] / _branch_name) { // have an entry for this branch name
-                   _existing_estimate = ((initial_values[terms.branch_length])[estimators.ApplyExistingEstimates.i])[_branch_name];
-
-                   if (Type(_existing_estimate) == "AssociativeList") {
-                       _set_branch_length_to = (((initial_values[terms.branch_length])[estimators.ApplyExistingEstimates.i])[_branch_name])[terms.fit.MLE];
-                        if (None != branch_length_conditions) {
-                            if (Abs(branch_length_conditions)) {
-                                _application_type = branch_length_conditions[estimators.ApplyExistingEstimates.i];
-
-                                if (Type(_application_type) == "String") {
-                                    if (_application_type == terms.model.branch_length_constrain ) {
-                                        estimators.ApplyExistingEstimates.df_correction += estimators.constrainBranchLength(_tree_name, _branch_name, model_descriptions[estimators.ApplyExistingEstimates.map[_branch_name]], _set_branch_length_to);
-                                        continue;
-                                    }
-                                    _set_branch_length_to = {};
-                                    _set_branch_length_to[terms.branch_length] = _existing_estimate[terms.fit.MLE];
-                                    _set_branch_length_to[terms.model.branch_length_scaler] = _application_type;
-                                    estimators.ApplyExistingEstimates.keep_track_of_proportional_scalers[_application_type] = 1;
-                                }
-                            }
-                        }
-
-                        estimators.ApplyExistingEstimates.df_correction += estimators.applyBranchLength(_tree_name, _branch_name, model_descriptions[estimators.ApplyExistingEstimates.map[_branch_name]], _set_branch_length_to);
-                    } else {
-                        if (Type(_existing_estimate) != "Unknown") {
-                            warning.log ("Incorrect type for the initial values object of for branch '" + _branch_name + "' : " + _existing_estimate);
-                        }
-                   }
-                }
-
-            }*/
-
         } else {
         	if (Type((initial_values[terms.branch_length])[estimators.ApplyExistingEstimates.i]) != "Unknown") {
         		warning.log ("Incorrect type for the initial values object for partition " + estimators.ApplyExistingEstimates.i
@@ -1099,17 +1077,20 @@ lfunction estimators.FitCodonModel(codon_data, tree, generator, genetic_code, op
         /**
             now replicate the local constraint for individual branches
         */
-
+
+
         alpha = model.generic.GetLocalParameter(mg_rev, utility.getGlobalValue("terms.parameters.synonymous_rate"));
         beta = model.generic.GetLocalParameter(mg_rev, utility.getGlobalValue("terms.parameters.nonsynonymous_rate"));
-         io.CheckAssertion("None!=`&alpha` && None!=`&beta`", "Could not find expected local synonymous and non-synonymous rate parameters in \`estimators.FitMGREV\`");
+        io.CheckAssertion("None!=`&alpha` && None!=`&beta`", "Could not find expected local synonymous and non-synonymous rate parameters in \`estimators.FitMGREV\`");
 
         apply_constraint: = component_tree + "." + node_name + "." + beta + ":=" + component_tree + "." + node_name + "." + alpha + "*" + new_globals[branch_map[node_name]];
 
         for (i = 0; i < components; i += 1) {
             component_tree = lf_components[2 * i + 1];
             ClearConstraints( * component_tree);
             branch_map = (option[utility.getGlobalValue("terms.run_options.partitioned_omega")])[i];
+
+
             component_branches = BranchName( * component_tree, -1);
             for (j = 0; j < Columns(component_branches) - 1; j += 1) {
                 /**

src/core/global_things.cpp

@@ -120,7 +120,7 @@ namespace hy_global {
                      kErrorStringDatasetRefIndexError ("Dataset index reference out of range"),
                      kErrorStringMatrixExportError    ("Export matrix called with a non-polynomial matrix argument"),
                      kErrorStringNullOperand          ("Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"),
-                     kHyPhyVersion  = _String ("2.5.9"),
+                     kHyPhyVersion  = _String ("2.5.10"),
 
                     kNoneToken = "None",
                     kNullToken = "null",

src/core/topology.cpp

@@ -384,8 +384,9 @@ _AssociativeList*    _TreeTopology::MainTreeConstructor  (_String const& parms,
                     lastNode = nodeStack.countitems ()-1;
                     parentNode = (node<long>*)nodeStack.get (lastNode);
                     if (mapping) {
-                        _FString * mapped_name = (_FString*)mapping->GetByKey (nodeName, STRING);
+                        _FString * mapped_name = (_FString*)mapping->GetByKey (nodeName.ChangeCase(kStringUpperCase), STRING);
                         if (mapped_name) {
+                            //printf ("%s => %s\n", nodeName.get_str(), mapped_name->get_str().get_str());
                             nodeName = _String (mapped_name->get_str());
                         }
                     }